Production of itaconic acid

ABSTRACT

The invention relates to a nucleic acid sequence encoding an itaconate transporting Major Facilitator Superfamily Transporter (MFST) gene sequence and the protein encoded thereby. Preferably said sequence is the nucleic acid that comprises the sequence of ATEG_09972.1 of  Aspergillus terreus  or homologues thereof. Overexpression of the protein enhances the production of itaconic acid in micro-organisms.

The invention relates to the field of microbial production, more specifically production of itaconic acid (itaconate), more specifically production of itaconate in micro-organisms.

Production and metabolism of itaconic acid in microbial cells has been studied extensively for several decades (Calam, C. T. et al., 1939, Thom. J. Biochem., 33:1488-1495; Bentley, R. and Thiessen, C. P., 1956, J. Biol. Chem. 226:673-720; Cooper, R. A. and Kornberg, H. L., 1964, Biochem. J., 91:82-91; Bonnarme, P. et al., 1995, J. Bacteriol. 117:3573-3578; Dwiarti, L. et al., 2002, J. Biosci. Bioeng. 1:29-33), but the metabolic pathway for itaconic acid has not been unequivocally established (Wilke, Th. and Vorlop, K.-D., 2001, Appl. Microbiol. Biotechnol. 56:289-295; Bonnarme, P. et al., 1995, J. Bacteriol. 177:3573-3578). Two complicating factors in this respect are that the biosynthesis route for itaconic acid is thought to occur both in the cytosol and the mitochondria (Jaklitsch, W. M. et al., 1991, J. Gen. Microbiol. Appl. 6:51-61) and that aconitase, the enzyme that interconverts citric acid into cis-aconitate, and vice versa, and other enzymes in the metabolic pathway have been found to be present in many isoforms in microbial cells.

Production of itaconic acid is now commercially achieved in Aspergillus terreus, which has physiological similarity to A. niger and A. oryzae. However, these latter two accumulate citric acid, due to the absence of cis-aconic acid decarboxylase (CAD) activity. Substrates used by these fungi include mono- and disaccharides, such as glucose, sucrose and fructose and starches, as they exist in forms that are degradable by the micro-organism, and molasses. Recently, it has been discovered that also glycerol is a useful substrate in itaconic acid production by A. terreus (U.S. Pat. No. 5,637,485).

The general scheme currently envisioned for itaconic acid biosynthesis is given in FIG. 1, wherein clearly the existence of the biosynthetic route both in the cytosol and the mitochondria is depicted and the connection between these two compartments. At several points of this scheme possibilities exist to try to improve the existing commercial production of itaconic acid in micro-organisms.

SUMMARY OF THE INVENTION

The invention comprises a nucleic acid sequence encoding an itaconate transporting Major Facilitator Superfamily Transporter (MFST) gene sequence (hereinafter “the itaconate transporter”). Preferably said nucleic acid comprises the ATEG_(—)09972.1 sequence of Aspergillus terreus as depicted in FIG. 3B, or a nucleic acid that shares more than about 70%, preferably more than about 80%, preferably more than about 90% sequence identity with the sequence of ATEG_(—)09972.1 as depicted in FIG. 3 b. In another embodiment, the invention comprises a protein encoded by said nucleic acid.

The invention further comprises a method for the production of itaconic acid. More specifically the invention relates to improved production of itaconic acid, comprising increasing the activity of a protein capable of transporting itaconate from the cytosol to the extracellular medium, in a suitable host cell. Preferably this is achieved by overexpression of a nucleic acid sequence encoding the protein of the invention. Preferably the said nucleic acid is derived from Aspergillus sp. such as, Aspergillus terreus, Aspergillus niger, Aspergillus nidulans, Aspergillus oryzae or Aspergillus fuminagates. According to a further preferred embodiment, the said nucleic acid is expressed in a suitable vector, under control of its own or other promoters.

Also comprised in the invention is a method as described above, wherein the above described transport of itaconic acid is further increased by increasing the intracellular itaconic acid, using at least one but preferably a combination of the following methods: 1. overexpression of the gene coding for the enzyme CAD (see EP 07112895) which catabolises cis-aconitate to itaconic acid, preferably wherein said gene is encoded by the nucleic acid sequence of ATEG 09971.1; 2. overexpression of a gene coding for a protein capable of transporting di/tricarboxylate, preferably cis-aconitate, citrate or isocitrate, from the mitochondrion to the cytosol, more preferably the diacrboxylate transporter encoded by the nucleic acid sequence of ATEG 09970.1 (see EP 08151584); 3. a method as described above, wherein the activity of a regulator protein that comprises a zinc finger and a fungal specific transcription factor domain is modulated. Preferably said regulator protein is the protein encoded by the nucleic acid sequence of ATEG 09969.1, located in the same gene cluster as the transporter of the invention. By using the above method 1 also organisms that do not or hardly produce itaconic acid like A. niger and A. oryzae due to the absence of endogenous cis-aconic acid decarboxylase (CAD) activity can be used since expression of the CAD gene will cause itaconic acid production.

Another embodiment of the present invention is formed by a host cell wherein a gene coding for an itaconate transporter is introduced. Preferably said gene comprises the nucleotide sequence of the invention encoding a transporter protein. A suitable host cell preferably is a host cell selected from filamentous fungi, yeasts and bacteria, more preferably from Escherichia coli, Aspergillus sp such as Aspergillus niger or Aspergillus terreus, citrate-producing hosts or lovastatin producing hosts. The invention further comprises a host cell as described above wherein the gene coding for a protein capable of transporting di/tricarboxylate, preferably cis-aconitate, citrate or isocitrate, from the mitochondrion to the cytosol, is co-expressed. The invention further comprises a host cell as described above, wherein the transported or produced cis-aconitate is catabolised to itaconic acid by overexpression of the gene encoding the enzyme CAD.

Further, the invention pertains to the use of the protein(s) transporting itaconate from the cytosol to the extracellular medium, for the production of itaconic acid by a suitable host cell. Also comprised in the invention is the use of said protein(s) combined with the proteins transporting di/tricarboxylate over the mitochondrial membrane, the regulator protein ATEG 09969.2 and/or the use of the CAD enzyme, for the production of itaconic acid in a suitable host cell.

LEGENDS TO THE FIGURES

FIG. 1: Postulated biosynthesis route(s) for itaconic acid in A. terreus. 1, Citrate synthase; 2, Aconitase; 3, cis-aconitic acid decarboxylase (itaconate-forming); 4, cis-aconitic acid decarboxylase (citraconate-forming); 5, citraconate isomerase; 6, mitochondrial dicarboxylate-tricarboxylate antiporter; 7, mitochondrial tricarboxylate transporter; 8, dicarboxylate transporter; 9, 2-methylcitrate dehydratase.

FIG. 2: Overview of Aspergillus terreus genome segment with the cluster of genes involved in production of itaconic acid and lovastatin ranging from ATEG 09961.1-ATEG 09975.1. The cluster contains the cis-aconitate decarboxylase (ATEG 09971.1) and the mitochondrial tricarboxylate transporter (ATEG 9970.1).

FIG. 3: Sequence of the Aspergillus terreus itaconate transporter: a. protein sequence, b. cDNA, c. genomic sequence.

FIG. 4: Sequence of the Aspergillus oryzae itaconate transporter: a. protein sequence, b. cDNA, c. genomic sequence.

DETAILED DESCRIPTION OF THE INVENTION

“Fungi” are herein defined as eukaryotic micro-organisms and include all species of the subdivision Eumycotina (Alexopoulos, C. J., 1962, In: Introductory Mycology, John Wiley & Sons, Inc., New York). The term fungus thus includes both filamentous fungi and yeast. “Filamentous fungi” are herein defined as eukaryotic micro-organisms that include all filamentous forms of the subdivision Eumycotina. These fungi are characterized by a vegetative mycelium composed of chitin, cellulose, and other complex polysaccharides. The filamentous fungi used in the present invention are morphologically, physiologically, and genetically distinct from yeasts. Vegetative growth by filamentous fungi is by hyphal elongation and carbon catabolism of most filamentous fungi are obligately aerobic. “Yeasts” are herein defined as eukaryotic micro-organisms and include all species of the subdivision Eumycotina that predominantly grow in unicellular form. Yeasts may either grow by budding of a unicellular thallus or may grow by fission of the organism.

The term “fungal”, when referring to a protein or nucleic acid molecule thus means a protein or nucleic acid whose amino acid or nucleotide sequence, respectively, naturally occurs in a fungus.

The term “gene”, as used herein, refers to a nucleic acid sequence containing a template for a nucleic acid polymerase, in eukaryotes, RNA polymerase II. Genes are transcribed into mRNAs that are then translated into protein.

“Expression” refers to the transcription of a gene into structural RNA (rRNA, tRNA) or messenger RNA (mRNA) with subsequent translation into a protein.

The term “vector” as used herein, includes reference to an autosomal expression vector and to an integration vector used for integration into the chromosome.

The term “expression vector” refers to a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of interest under the control of (i.e., operably linked to) additional nucleic acid segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and may optionally include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, and the like. Expression vectors are generally derived from plasmid or viral DNA, or may contain elements of both. In particular an expression vector comprises a nucleotide sequence that comprises in the 5′ to 3′ direction and operably linked: (a) a yeast-recognized transcription and translation initiation region, (b) a coding sequence for a polypeptide of interest, and (c) a yeast-recognized transcription and translation termination region. “Plasmid” refers to autonomously replicating extrachromosomal DNA which is not integrated into a microorganism's genome and is usually circular in nature.

An “integration vector” refers to a DNA molecule, linear or circular, that can be incorporated in a microorganism's genome and provides for stable inheritance of a gene encoding a polypeptide of interest. The integration vector generally comprises one or more segments comprising a gene sequence encoding a polypeptide of interest under the control of (i.e., operably linked to) additional nucleic acid segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and one or more segments that drive the incorporation of the gene of interest into the genome of the target cell, usually by the process of homologous recombination. Typically, the integration vector will be one which can be transferred into the host cell, but which has a replicon that is nonfunctional in that organism. Integration of the segment comprising the gene of interest may be selected if an appropriate marker is included within that segment.

“Transformation” and “transforming”, as used herein, refer to the insertion of an exogenous polynucleotide into a host cell, irrespective of the method used for the insertion, for example, direct uptake, transduction, f-mating or electroporation. The exogenous polynucleotide may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome.

By “host cell” is meant a cell that contains a vector or recombinant nucleic acid molecule and supports the replication and/or expression of the vector or recombinant nucleic acid molecule. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, fungus, plant, insect, amphibian, or mammalian cells. Preferably, host cells are fungal cells.

Key in the biosynthetic pathway for itaconic acid is the localisation of the various substrates. It is thought that production of itaconic acid mainly occurs in the cytosol (see FIG. 1). In many biochemical pathways, the end-product is inhibiting its own production to prevent excess end-product in the biological system. Excess end-product will not only lead to loss of energy in an economical sense, it can also give rise to unwanted side effects such as toxicity. It is contemplated that by depleting the cell of itaconic acid the formation of new itaconic acid will continue without end-product inhibition, thus giving—in total—an increase yield of itaconic acid. Additionally the present invention enables a more simple way of harvesting the itaconic acid due to its presence in the extracellular medium. This also enables continuous fermentation culture.

Also provided are functional homologues of the ATEG_(—)09972.1 sequences, that are 50% or more identical to the sequence of FIG. 3 b, preferably 60% or more, more preferably 70% or more, more preferably 80% or more, more preferably 90% or more and most preferably 95% or more identical. Functional in the term functional homologues means that the homologous protein has an itaconic acid/itaconate transporter function i.e. is able to transport itaconate over the cell membrane.

The term “sequence identity,” as used herein, is generally expressed as a percentage and refers to the percent of amino acid residues or nucleotides, as appropriate, that are identical as between two sequences when optimally aligned. For the purposes of this invention, sequence identity means the sequence identity determined using the well-known Basic Local Alignment Search Tool (BLAST), which is publicly available through the National Cancer Institute/National Institutes of Health (Bethesda, Md.) and has been described in printed publications (see, e.g., Altschul et al., J. MoI. Biol, 215(3), 403-10 (1990)). Preferred parameters for amino acid sequences comparison using BLASTP are gap open 11.0, gap extend 1, Blosum 62 matrix.

Every nucleic acid sequence herein that encodes a polypeptide also, by reference to the genetic code, describes every possible silent variation of the nucleic acid. The term “conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or conservatively modified variants of the amino acid sequences due to the degeneracy of the genetic code.

The term “degeneracy of the genetic code” refers to the fact that a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations” and represent one species of conservatively modified variation.

The present inventors have found a method for increasing the production of itaconic acid, by increasing the activity of the protein capable of transporting itaconate from the cytosol to the extracellular medium, leading to increased recovery of itaconic acid, produced by a suitable micro-organism. The protein is further defined as a protein capable of transporting itaconic acid.

Preferably, the itaconate transporter is the itaconate transporter of Aspergillus terreus, as is found in the itaconate/lovastatin gene cluster (see FIG. 2), which is represented by the nucleic acid sequence found in ATEG_(—)09972.1, which is disclosed in FIGS. 3 b and 3 c, for the cDNA and genomic sequence, respectively.

Further example of an itaconate transporter that could also be used in the present invention is the homologous gene denominated BAE57135.1 from A. oryzae, as depicted in FIGS. 4 a, 4 b and 4 c. The produced itaconic acid can be recovered from the extracelluar medium using methods know to a person skilled in the art and as described by Wilke et al. (Wilke, Th. and Vorlop, K.-D., 2001, Appl. Microbiol. Biotechnol. 56:289-295). One preferred way of increasing the activity of said protein(s) is by overexpression of a gene(s) encoding said protein(s), preferably wherein said gene is ATEG_(—)09972.1.

Overexpression can be effected in several ways. It can be caused by transforming the micro-organism with a gene coding for the enzyme. Alternatively, other methods can be used for effecting an increase in the activity of said enzyme. One possible way is to provide a stronger promoter in front of and regulating expression of the endogenous gene. This can be achieved by use of a strong heterologous promoter or by providing mutations in the endogenous promoter. An increased activity of the enzyme can also be caused by removing possible inhibiting regulatory proteins, e.g. by inhibiting the expression of such proteins. The person skilled in the art will know other ways of increasing the activity of the above mentioned enzyme.

The production of itaconic acid can be further optimised by combining the product secretion and recovery as described above, with overexpression of di/tricarboxylate transporters, capable of transporting, among others, cis-aconitate, citrate or isocitrate from the mitochondrion to the cytosol, preferably the gene encoded by the nucleic acid sequence of ATEG_(—)09970.1. These subsequent processes will lead to an increase in cis-aconitate in the cytosol, which can be further converted to itaconic acid, using overexpression of the gene encoding the enzyme CAD (EC 4.1.1.6). “CAD” is defined as the enzyme, or a nucleotide sequence encoding for the enzyme cis-aconitate decarboxylase (CAD), such as the enzyme encoded by the nucleic acid sequence of ATEG_(—)09971.1, this further comprises enzymes with similar activities (see EP07112895).

Even further optimisation of the present invention can be achieved by modulating the activity of the regulator protein that comprises a zinc finger and a fungal specific transcription factor domain as can be found on the gene cluster that also comprises ATEG_(—)09970, wherein this regulator protein is indicated as ATEG_(—)09969.1 (see FIG. 2).

The above described processes alone or in combination lead to a subsequent increase of itaconic acid (see FIG. 1). Another advantage of the invention is an improved method to recover the produced itaconic acid by increasing the release in the extracellular media. The combination of improved production and improved recovery leads to an increase in itaconic acid yield by a suitable host. The above described genes are preferably derived from Aspergillus sp. like, Aspergillus terreus, Aspergillus niger, Aspergillus nidulans, Aspergillus oryzae or Aspergillus fuminagates. However, it is also possible to derive the gene from other itaconate producing micro-organisms such as Ustilago zeae, Ustilago maydis, Ustilago sp., Pseudozyma antarctica, Candida sp., Yarrowia lipolytica, and Rhodotorula sp.

In another aspect of the invention, micro-organisms overexpressing at least one but alternatively a combination of the above mentioned nucleotide sequences, encoding at least a protein capable of transporting itaconate from the cytosol to the extracellular medium, are produced and used for increased production of itaconic acid. More preferably micro-organisms overexpressing a protein that transports itaconate combined with protein(s) that transport di/tricarboxylates from the mitochondrion to the cytosol and/or the CAD enzyme are used to further improve the production of itaconic acid.

Micro-organisms used in the invention are preferably micro-organisms that naturally produce itaconic acid. Preferably overexpression of the genes encoding the above described protein(s) and enzyme(s) is accomplished in filamentous fungi, yeasts and/or bacteria, such as, but not limited to Aspergillus sp., such as the fungi A. terreus, A. itaconicus and A. niger, Aspergillus nidulans, Aspergillus oryzae or Aspergillus fuminagates, Ustilago zeae, Ustilago maydis, Ustilago sp., Candida sp., Yarrowia lipolytica, Rhodotorula sp. and Pseudozyma antarctica, the bacterium E. coli and the yeast Saccharomyces cerevisiae. Especially preferred are heterologous citric acid producing organisms in which the substrates are available in the host organism.

Recently (see US 2004/0033570) it has also been established that the so-called D4B segment of Aspergillus terreus, which comprises the CAD gene is responsible for the synthesis of lovastatin (see FIG. 2). Thus, it is submitted that also these micro-organisms which are known to produce lovastatin would be suitable candidates for the production of itaconic acid. Such micro-organisms include Monascus spp. (such as M. ruber, M. purpureus, M. pilosus, M. vitreus and M. pubigerus), Penicillium spp. (such as P. citrinum, P. chrysogenum), Hypomyces spp., Doratomyces spp. (such as D. stemonitis), Phoma spp., Eupenicillium spp., Gymnoascus spp., Pichia labacensis, Candida cariosilognicola, Paecilomyces virioti, Scopulariopsis brevicaulis and Trichoderma spp. (such as T. viride).

Consequently also the CAD encoding part of the D4B segment and the enzyme with CAD activity for which it codes from these above-mentioned lovastatin producing micro-organisms are deemed to be suitable for use in the present invention. It further is contemplated that a heterologous organism, which in nature does not or hardly produce itaconic acid like Aspergillus niger or Aspergillus oryzae can be used when providing such an organism with a functional pathway for expression of itaconic acid, by overexpression of the above mentioned genes.

Recombinant host cells described above can be obtained using methods known in the art for providing cells with recombinant nucleic acids. These include transformation, transconjugation, transfection or electroporation of a host cell with a suitable plasmid (also referred to as vector) comprising the nucleic acid construct of interest operationally coupled to a promoter sequence to drive expression. Host cells of the invention are preferably transformed with a nucleic acid construct as further defined below and may comprise a single but preferably comprises multiple copies of the nucleic acid construct. The nucleic acid construct may be maintained episomally and thus comprise a sequence for autonomous replication, such as an ARS sequence. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9: 968-975) plasmids. Preferably, however, the nucleic acid construct is integrated in one or more copies into the genome of the host cell. Integration into the host cell's genome may occur at random by illegitimate recombination but preferably the nucleic acid construct is integrated into the host cell's genome by homologous recombination as is well known in the art of fungal molecular genetics (see e.g. WO 90/14423, EP-A-0 481 008, EP-A-0 635 574 and U.S. Pat. No. 6,265,186) Most preferably for homologous recombination the ku70Δ/ku80Δ techniques is used as described for instance in WO 02/052026 and Krappmann, 2007, Fungal Biol. Rev. 21:25-29).

Transformation of host cells with the nucleic acid constructs of the invention and additional genetic modification of the fungal host cells of the invention as described above may be carried out by methods well known in the art. Such methods are e.g. known from standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, or F. Ausubel et al, eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York (1987). Methods for transformation and genetic modification of fungal host cells are known from e.g. EP-A-0 635 574, WO 98/46772, WO 99/60102 and WO 00/37671.

In another aspect the invention relates to a nucleic acid construct comprising a nucleotide sequence encoding at least an itaconate transporter as defined above and usable for transformation of a host cell as defined above. In the nucleic acid construct, the coding nucleotide sequence(s) preferably is/are operably linked to a promoter for control and initiation of transcription of the nucleotide sequence in a host cell as defined below. The promoter preferably is capable of causing sufficient expression of the itaconate transporters transporting itaconate from the cytosol to the extracellular medium and/or the di/tricarboxylate transporters transporting tricarboxylates from the mitochondrion and/or the CAD enzyme(s), described above, in the host cell. Promoters useful in the nucleic acid constructs of the invention include the promoter that in nature provides for expression of the coding genes. Further, both constitutive and inducible natural promoters as well as engineered promoters can be used. Promoters suitable to drive expression of the genes in the hosts of the invention include e.g. promoters from glycolytic genes (e.g. from a glyceraldehyde-3-phosphate dehydrogenase gene), ribosomal protein encoding gene promoters, alcohol dehydrogenase promoters (ADH1, ADH4, and the like), promoters from genes encoding amylo- or cellulolytic enzymes (glucoamylase, TAKA-amylase and cellobiohydrolase). Other promoters, both constitutive and inducible and enhancers or upstream activating sequences will be known to those of skill in the art. The promoters used in the nucleic acid constructs of the present invention may be modified, if desired, to affect their control characteristics. Preferably, the promoter used in the nucleic acid construct for expression of the genes is homologous to the host cell in which genes are expressed.

In the nucleic acid construct, the 3′-end of the coding nucleotide acid sequence(s) preferably is/are operably linked to a transcription terminator sequence. Preferably the terminator sequence is operable in a host cell of choice. In any case the choice of the terminator is not critical; it may e.g. be from any fungal gene, although terminators may sometimes work if from a non-fungal, eukaryotic, gene. The transcription termination sequence further preferably comprises a polyadenylation signal.

Optionally, a selectable marker may be present in the nucleic acid construct. As used herein, the term “marker” refers to a gene encoding a trait or a phenotype which permits the selection of, or the screening for, a host cell containing the marker. A variety of selectable marker genes are available for use in the transformation of fungi. Suitable markers include auxotrophic marker genes involved in amino acid or nucleotide metabolism, such as e.g. genes encoding ornithine-transcarbamylases (argB), orotidine-5′-decarboxylases (pyrG, URA3) or glutamine-amido-transferase indoleglycerol-phosphate-synthase phosphoribosyl-anthranilate isomerases (trpC), or involved in carbon or nitrogen metabolism, such e.g. niaD or facA, and antibiotic resistance markers such as genes providing resistance against phleomycin, bleomycin or neomycin (G418). Preferably, bidirectional selection markers are used for which both a positive and a negative genetic selection is possible. Examples of such bidirectional markers are the pyrG (URA3), facA and amdS genes. Due to their bidirectionality these markers can be deleted from transformed filamentous fungus while leaving the introduced recombinant DNA molecule in place, in order to obtain fungi that do not contain selectable markers. This essence of this MARKER GENE FREE™ transformation technology is disclosed in EP-A-0 635 574, which is herein incorporated by reference. Of these selectable markers the use of dominant and bidirectional selectable markers such as acetamidase genes like the amdS genes of A. nidulans, A. niger and P. chrysogenum is most preferred. In addition to their bidirectionality these markers provide the advantage that they are dominant selectable markers that, the use of which does not require mutant (auxotrophic) strains, but which can be used directly in wild type strains.

Optional further elements that may be present in the nucleic acid constructs of the invention include, but are not limited to, one or more leader sequences, enhancers, integration factors, and/or reporter genes, intron sequences, centromers, telomers and/or matrix attachment (MAR) sequences. The nucleic acid constructs of the invention may further comprise a sequence for autonomous replication, such as an ARS sequence. Suitable episomal nucleic acid constructs may e.g. be based on the yeast 2μ or pKD1 (Fleer et al., 1991, Biotechnology 9: 968-975) plasmids. Alternatively the nucleic acid construct may comprise sequences for integration, preferably by homologous recombination (see e.g. WO98/46772). Such sequences may thus be sequences homologous to the target site for integration in the host cell's genome. The nucleic acid constructs of the invention can be provided in a manner known per se, which generally involves techniques such as restricting and linking nucleic acids/nucleic acid sequences, for which reference is made to the standard handbooks, such as Sambrook and Russel (2001) “Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, or F. Ausubel et al, eds., “Current protocols in molecular biology”, Green Publishing and Wiley Interscience, New York (1987).

In a further aspect the invention relates to fermentation processes in which the transformed host cells of the invention are used for the conversion of a substrate into itaconic acid. A preferred fermentation process is an aerobic fermentation process. The fermentation process may either be a submerged or a solid state fermentation process.

In a solid state fermentation process (sometimes referred to as semi-solid state fermentation) the transformed host cells are fermenting on a solid medium that provides anchorage points for the fungus in the absence of any freely flowing substance. The amount of water in the solid medium can be any amount of water. For example, the solid medium could be almost dry, or it could be slushy. A person skilled in the art knows that the terms “solid state fermentation” and “semi-solid state fermentation” are interchangeable. A wide variety of solid state fermentation devices have previously been described (for review see, Larroche et al., “Special Transformation Processes Using Fungal Spores and Immobilized Cells”, Adv. Biochem. Eng. Biotech., (1997), Vol 55, pp. 179; Roussos et al., “Zymotis: A large Scale Solid State Fermenter”, Applied Biochemistry and Biotechnology, (1993), Vol. 42, pp. 37-52; Smits et al., “Solid-State Fermentation-A Mini Review, 1998), Agro-Food-Industry Hi-Tech, March/April, pp. 29-36). These devices fall within two categories, those categories being static systems and agitated systems. In static systems, the solid media is stationary throughout the fermentation process. Examples of static systems used for solid state fermentation include flasks, petri dishes, trays, fixed bed columns, and ovens. Agitated systems provide a means for mixing the solid media during the fermentation process. One example of an agitated system is a rotating drum (Larroche et al., supra). In a submerged fermentation process on the other hand, the transformed fungal host cells are fermenting while being submerged in a liquid medium, usually in a stirred tank fermenter as are well known in the art, although also other types of fermenters such as e.g. airlift-type fermenters may also be applied (see e.g. U.S. Pat. No. 6,746,862).

Preferred in the invention is a submerged fermentation process, which is performed in a fed-batch or repeated (fed-) batch mode. In a fed-batch fermentation there is a continuous input of feed containing a carbon source and/or other relevant nutrients in order to improve itaconic acid yields. The input of the feed can, for example, be at a constant rate or when the concentration of a specific substrate or fermentation parameter falls below some set point. In a repeated batch fermentation the culture is harvested at regular time-intervals by stopping the fermentation and retrieving the produced product from the medium. Next to refreshing the medium often also part of the microbial culture is discarded, while the rest is used as a new inoculum for a following batch culture.

It is preferred to use a host cell that naturally would contain the enzymes/transporters of the itaconic acid pathway as depicted in FIG. 1, and the enzymes/transporters of the citric acid pathways in the cytosol and mitochondrion. However, if the host would lack one or more of these genes, they can be co-introduced with the above described enzymes and proteins. Such a co-introduction can be performed by placing the nucleotide sequence of such a gene on the same plasmid vector as the above described genes, or on a separate plasmid vector.

Further, since the itaconic acid pathway is located partly in the cytosol and partly in the mitochondrion, it is contemplated that overexpression of the genes/enzymes in either or both of those compartments would be desirable. The person skilled in the art will know how to achieve overexpression in the cytosol or mitochondria by using the appropriate signal sequences.

EXAMPLES Example 1 Construction of Micro-Array

An anonymous clone/EST-based array approach was taken according to the following scheme:

An A. terreus micro-array was made composed of a clone-based and an EST-based array.

Materials and Methods Construction Micro-Array

Isolation of Chromosomal DNA from A. Terreus

A. terreus was cultivated overnight in a shake flask in enriched minimal medium at 33° C. and 250 rpm. Enriched minimal medium (pH 5.5) is mineral medium (MM) supplemented with 0.5% yeast extract and 0.2% casamino acids. The composition of MM was: 0.07 M NaNO₃, 7 mM KCl, 0.11 M KH₂PO₄, 2 mM MgSO₄, and 1 ml/l of trace elements (1000*stock solution: 67 mM ZnSO₄, 178 mM H₃BO₃, 25 mM MnCl₂, 18 mM FeSO₄, 7.1 mM CoCl₂, 6.4 mM CuSO₄, 6.2 mM Na₂MoO₄, 174 mM EDTA).

Mycelium was harvested after 22 hours and frozen in liquid nitrogen. Chromosomal DNA was isolated from 4.5 g mycelium following the protocol described below.

-   -   Grind 0.5-1.0 g mycelium under liquid nitrogen using the         membrane disrupter.         -   Place polypropylene tubes (Greiner) with 1.5 ml             water-saturated phenol, 1 ml TNS, 1 ml PAS and 0.5 ml 5×RNB             in a water bath at 55° C., add the still frozen mycelium to             the tubes and vortex every 20 seconds for totally 2-4             minutes.         -   TNS: triisopropyl naphthalene sulphonic acid, 20 mg/ml in             water, freshly prepared         -   PAS: 4 aminosalisylic acid, 120 mg/ml in water, freshly             prepared         -   5×RNB: 60.55 g Tris, 36.52 g NaCl, 47.55 g EGTA in 500 ml             water (pH=8.5)     -   Add 1 ml sevag (24:1 chloroform:isoamyl alcohol) and vortex with         intervals for another 1-2 minutes.     -   Spin for 10 min. in the tabletop centrifuge at 4° C. at maximum         velocity.     -   Extract the water-phase once again with phenol-sevag and twice         with sevag. GENTLY, AVOID SHEARING!     -   Precipitate the DNA with 2 volumes ethanol. Spin directly for 10         min. in the tabletop centrifuge.     -   Drain the tube, dry it with Kleenex and resuspend the pellet in         500 μl Tris/EDTA. Transfer to a microvial.     -   Extract with phenol-sevag until interface stays clean. Then         extract once with sevag.     -   Precipitate with 2 volumes ice-cold ethanol, spin down and         resuspend the pellet in 100-200 μl TE with 50 μg/ml RNase.         Construction of Clone-Based gDNA Library         The gDNA library was prepared as follows:

Chromosomal A. terreus DNA was sheared into fragments of size 1.5-2.5 kb

-   -   The sheared DNA was subsequently size fractionated, end-repaired         (Lucigen), and ligated into blunt-end pSMART-HC-Amp vectors         (Lucigen).     -   The ligated constructs were transformed into E. coli DH 10b     -   Colony PCR was performed on 96 transformants to check that >90%         of the inserts had the correct size     -   Sequence analysis (short run) was performed on 20 clones to         confirm their diversity and fungal origin     -   Colony picking of 20,000 amp-resistant colonies was carried out         into 96-well microtiter plates containing TY medium+100 μg/ml         ampicillin         The 20.000 clones were replicated into 96-well microtiter         plates. The ordered libraries are stored as glycerol stocks at         −80° C.         Generation of mRNA for cDNA Library Construction         Precultures: A. terreus spores (10⁶-10⁷/ml) were inoculated into         100 ml B medium (2 g/l NH4NO3; 1 g/l MgSo4*7H2O; 0.008 g/l         ZnSO4*7H2O; 0.015 g/l CuSO4*5H2O; 1.5 ppm FeSO4*5H2O; 0.08 g/l         KH2PO4; 10 g/l CaCl2*2H2O, set to pH 3.1 with HCl) containing 20         g/l glucose, and incubated for 24-48 hours at 37° C. at 250 rpm.         Production cultures (B medium containing 100 g/l glucose) were         inoculated 1/10 (v/v) for 2-days cultivations and 1/25 (v/v) for         3-day cultivations. After 2-3 days cultivation mycelium was         harvested, filtered over miracloth, washed with 0.2 M sodium         phosphate buffer (pH 6.5), frozen in liquid nitrogen and stored         at −80° C.         Isolation of mRNA from A. Terreus     -   grind mycelium with mortar and pestle under liquid nitrogen; add         100 μl β-mercaptoethanol before grinding to inactivate RNAse     -   transfer powder to cooled plastic tube (1.0 g per tube); keep         mycelium frozen     -   add 4 ml Trizol and vortex till homogenous     -   add 0.4 ml chloroform and vortex     -   centrifuge for 20-30 min. at 3700 rpm, 4° C.     -   transfer supernatant to Eppendorf tubes (1.2 ml per tube)     -   add 0.7 ml per 1.2 ml supernatant     -   centrifuge in eppendorf centrifuge for 15 min. at 14.000 rpm, 4°         C.     -   wash pellet with 1 ml 70% ethanol     -   centrifuge 5 min., 14.000 rpm, 4° C.     -   air-dry pellet and resuspend in 0.2 ml water     -   store RNA samples at −80° C.         Construction of cDNA library         The cDNA library was prepared as follows:     -   The RNA was run on gel to determine the quality of the sample     -   polyT-primed cDNA was prepared from the total RNA provided         (RT-PCR reaction using superscript and dT primers     -   The cDNA was size fractionated to give fragments of size 1.0-1.5         kb     -   The fragments were end-repaired (Lucigen), and ligated into         blunt-end p SMART-HC-kan vectors (Lucigen).     -   Restriction analysis of 96 clones was performed to check the         insert size and the % of transformants which had the correct         insert size     -   Sequence analysis (short run) of 20 clones was performed to         confirm diversity and fungal origin     -   5,000 kanamycin-resistant colonies were picked into microtiter         plates         The 5000 cDNA clones were replicated into 96-well microtiter         plates. The ordered libraries were stored as glycerol stocks at         −80° C.

Construction of the A. Terreus Clone-Based Array

PCR fragments were generated from the different clones from the gDNA (20,000 clones) and cDNA (5,000 clones) library by mass 96 well PCR (50 μl/well, Lucigen SMART-SR1/SL1 primers with 5′-C6-aminolinkers, SuperTaq and buffer from HT Biotech. Ltd, dNTP's (Roche 11 969 064 001), pintool dipped template from grown colony plates).

All above PCR products were purified by 96 well precipitation (isopropanol and 96% ethanol wash), speedvac dried, dissolved in 15 μl 3×SSC/well and spotted with quill pins (Telechem SMP3) on CSS100 silylated aldehyde glass slides (Telechem, USA) using a SDDC2 Eurogridder (ESI, Canada). During spotting, aminolinkers of PCR products will covalently link with aldehyde groups of the coated slides.

gDNA and cDNA PCR products were spotted on two separate slides (slide a: 1st 10,000 gDNA's+5000 cDNA's; slide b: 2nd 10,000 gDNA's+same 5000 cDNA's).

For the clone-based array a genomic library was constructed. A total of 20,000 clones containing chromosomal fragments was generated, 90% of which had an average insert size of 1.5-2.5 kb. This resulted in a full genome coverage of 64% (Akopyants et al., 2001).

For the EST-based array a cDNA library of in total 5000 cDNA clones was constructed, 70% of which had an average insert size of 1.0-1.5 kb. This so-called EST-based approach has the advantage that it will be enriched for the genes expressed under the selected (itaconic acid producing) conditions. Moreover, in the EST-based approach per clone (and thus spot) only a single gene is represented in eukaryotes.

The complete micro-array, thus consisting of 20,000 genomic DNA clones and 5,000 cDNA clones was composed of an A and a B glass slide. Both slides contained the same 5,000 cDNA spots. The A and B slide each contained 10,000 of the gDNA spots.

Example 2 Generation of the Different RNA Samples by Fermentation

Materials and Methods Fermentation and mRNA Isolation

Fermentation Conditions of A. Terreus

5-Liter controlled batch fermentations were performed in a New Brunswick Scientific Bioflow 3000 fermentors. The following conditions were used unless stated otherwise:

-   -   37° C.     -   pH start 3.5 set point 2.3     -   DO set points Day 1: 75%         -   Day 2, 3, 4: 50%         -   Subsequent days: 25%     -   Preculture: 100 ml of the same medium as used in the         fermentation medium (10⁷ spores/ml) in 500 ml Erlenmeyer flask         with baffles, overnight, 37° C., 150 rpm     -   pH control: 4M KOH (Base), 1.5 M H₃ PO₄ (Acid)     -   Antifoam: Struktol (Schill & Seilacher)

Fermentation Medium Compositions:

Per litre: 2.36 g of NH₄SO₄, 0.11 g of KH₂PO₄, 2.08 g of MgSO₄*7H₂O, 0.13 g of CaCl₂*2H₂O, 0.074 g of NaCl, 0.2 mg of CuSO₄*5H₂O, 5.5 mg of Fe(III) SO₄*7H₂O, 0.7 mg of MnCl₂*4H₂O and 1.3 mg of ZnSO₄*7H₂O and 100 g of glucose as a carbon source. All media were prepared in demineralised water. Isolation of mRNA from A. Terreus

See mRNA isolation protocol described in Example 1

Determination of the Itaconate Concentration by HPLC

5 μl of a 10-times diluted supernatant sample (split ratio 1:3) was separated using a Waters 2695 Separations module on a reversed-phase Develosil 3 μm RP-Aqueous C30 140A column (150×3 mm) (Phenomenex p/n CH0-6001) at 25° C. using the solvent gradient profile (flow rate was 0.4 ml/min) shown in Table 1.

TABLE 1 Solvent gradient of the RP-UV method. A B Time (20 mM NaH₂PO₄ (Acetonitril) (min) pH 2.25) (%) (%) 0 100 0 10 100 0 15 95 5 20 95 5 21 100 0 30 100 0 Compounds were detected by UV at 210 nm using a Waters 2487 Dual wavelength Absorbance detector (Milford, MA, USA).

Itaconate Productivity

Itaconate productivity at a certain time point was calculated as the slope of the regression line between that particular time point and the time points right before and after that time point. To this end of 6-10 supernatant samples of the different fermentations, the itaconate concentrations were determined by HPLC.

For the transcriptomics approach it is essential to have RNA samples from fermentations that result in the production of different amounts of itaconate. Therefore a literature survey was performed in order to identify medium components and/or physicochemical conditions that affect the amount of itaconate produced by A. terreus. Although many conflicting reports were found regarding the effect that a specific parameter has on itaconic acid production, 4 key overall parameters were identified from this literature survey, i.e. (i) carbon source, (ii) pH, (iii) trace element (i.e. Mn) concentration and (iv) oxygen tension. Fermentations with A. terreus varying principally in these four parameters were performed on a mineral salts medium to ensure that the elemental limitations required for itaconate production would be achieved. Table 2 presents an overview of the fermentations performed in this study.

TABLE 2 Overview of the fermentations performed in order to generate RNA samples for transcriptome analysis. Fermen- Max. Max. tation Fermen- Itaconic Biomass run tation Environmental condition acid (g/l) (gDWT/kg) First 1 Glucose (100 g/l) (control) 16.1 12.7 Run 2 Fructose as C-source 8.84 13.7 3 Maltose as C-source 13.9 12.1 Second 4 Glucose (100 g/l) pH start 25.8 11.6 run 3.5, set point 2.3 (control) 5 pH set 3.5 8.7 16.5 6 pH start 3.5 no set point 30.6 8.7 Third 7 Low glucose (30 g/l) 11.1 6.7 run 8 O₂ set point 25% 47.2 12.0 9 5* higher Mn 20.3 13.8 Fourth 10 Glucose (100 g/l) (control) 26.9 17.9 run 11 pH set 4.5 0.1 20.4 12 O₂ set point 10% 52.9 10.6 The reference fermentation is on 100 g/l glucose, dO2, day 1, 75%; day 2-4, 50%, day 5 and further 25%, pH start 3.5, set point at 2.3.

As shown in Table 2, a considerable variation in the amount of itaconate is produced in this set of fermentations, ranging from almost no itaconate (fermentation #11; pH 4.5) to about 50 g/l itaconate (#8 and #12; 02 set point 25% and 10% respectively).

Of each fermentation 2 to 5 samples were harvested for isolation of mRNA.

From in total 23 fermentation samples mRNA could be isolated. Of 7 samples, mRNA was isolated twice independently. It proved to be especially difficult (impossible) to extract RNA from the samples taken in the stationary phase. A number of samples showed partial degradation of the RNA. Although no mRNA could be isolated from the samples from fermentations #6 and #12, the remaining samples still covered the complete range of itaconate production (Table 3).

TABLE 3 List of 30 mRNA samples from various fermentation conditions that were used for transcriptome analysis. The samples marked with asterix were the samples used for the differential expression data analysis. Itaconic Sample Fermentation RNA Itaconic acid acid RNA no. condition id EFT (hours) (g/l) Productivity quality R3 gluc100  1.3.a 50.3 14.6 0.117 ok R4 gluc100  1.4.a 74.8 16.1 0.060 ok R5 fruc100  2.3.a 50.3  8.2 0.082 ok R6 fruc100  2.3.b 50.3  8.2 0.082 ok R7 fruc100  2.4.a  75.05  8.6 −0.013 ok R8 malt100  3.3.a 50.3 7  0.355 ok R9 malt100  3.4.a 75   12.1 0.220 ok R10 pH-i3.5  4.3.a  53.25 25.8 0.146 part degr R11 pH-i3.5  4.3.b  53.25 25.8 0.146 part degr R12 pH-i3.5  4.4.a 73   24   −0.153* ok R13 pH-c3.5  5.3.a 53.5  7.5 −0.042 ok R14 pH-c3.5  5.3.b 53.5  7.5 −0.042 ok R15 pH-c3.5  5.4.a  73.25  7.9 0.035 ok R16 gluc30  7.2.a  30.25 9  0.317 ok R1 gluc30  7.3.a 43.5 10   0.030 ok R17 gluc30  7.3.a 43.5 10   0.030 ok R18 O2s25%  8.2.a 30.5 36*  0.824* ok R19 O2s25%  8.4.a  78.25 46   0.029 part degr R20 5xMn  9.2.a  30.75 1  0.194 ok R21 5xMn  9.2.b  30.75 1  0.194 ok R22 5xMn  9.3.a 53.5 10   0.496 part degr R23 5xMn  9.3.b 53.5 10   0.496 part degr R24 5xMn  9.4.a 78.5 19   0.189 part degr R25 5xMn  9.4.b 78.5 19   0.189 part degr R26 5xMn  9.5.a  93.25 20   0.106 ok R2 Gluc100 10.3.a 51.5 14.7 0.256 ok R27 Gluc100 10.3.a 51.5 14.7 0.256 ok R28 Gluc100 10.4.a 74   19.5 0.085 ok R29 Gluc100 10.5.a 100.4  22   0.177 part degr R30 Gluc100 10.5.b 100.4  22   0.177 part degr R31 pH 4.5 11.3.a 51.5   0.04* −0.001 ok R32 pH 4.5 11.4.a 74     0.05* 0.003 ok

Example 3 Transcriptome Analysis, Data Analysis of the Array Data Materials and Methods Transcriptome Analysis, Data Normalization and Data Analysis

Labeling of RNA and gDNA

Total RNA's (5 μg/30 μl reaction), isolated from various A. terreus cultures (strain NRRL 1960, BASF) with differential itaconate production, were labelled with amino-allyl-dUTP (0.75 μM aa-dUTP final conc., Sigma A0410), using 3 μl 50 μM oligo p(dT)₁₅ primer (La Roche, 814270), unlabelled dNTP's (added to 1.25 μM final conc. for each dNTP), 2 μl Superscript II Reverse Transcriptase and buffer (Life Technologies, 10297-018: primer annealing 10 min 70° C., transcriptase 180 min 42°). After RNA hydrolysis (3 μl 2.5M NaOH, 30 min 37°, 3 μl 2.5 M HAc) the aa-dUTP labelled cDNA was directly purified (below).

As a reference for correcting slide differences (spotting, labeling-, hybridization- and scan efficiency), gDNA (0.5 μg/reaction) of Aspergillus terreus (strain NRRL 1960, BASF) was labelled with aa-dUTP, using dNTP's (conc. as above), Klenov-DNA Polymerase and buffer (Bioprime kit, Invitrogen 18094-011: primer annealing 5 min 96° C., polymerase 90 min 37°).

The aa-dUTP-labelled cDNA or gDNA was purified (QIAquick column, Qiagen 28106), speedvac dried, dissolved (4.5 μl 0.1 M Na₂CO₃), coupled with 4.5 μl Cy5-NHS-ester for cDNA, or 4.5 μl Cy3-NHS-ester for gDNA (Amersham/GE-Healthcare PA25001 or PA23001 respectively, each in 73 μl DMSO) for 60 min at 20° C., diluted with 10 μl of water, and again purified on Autoseq G50 columns (GE-Healthcare 27-5340).

Array Blocking, (Pre) Hybridization and Image Analysis

Before hybridization with the array produced as described above, slides were blocked (removal surplus of spotted PCR products and blocking of free aldehyde groups) by 3× quickly washing (20° C.) with Prehyb buffer and 45 min incubation (42° C.) in PreHyb buffer (5×SSC, 1% BSA, 0.1% SDS). After 4 washes in water, spotted PCR products were denatured by dipping the slides 5 sec in boiling water and drying them with a N₂-gas-pistol.

The Cy5- and Cy3-labelled sample were combined, 8 μl 25 μg/μl yeast tRNA (Invitrogen, 15401-029) and 4 μl 5 μg/μl poly-dA/dT (Amersham 27-7860) were added, the mixture was speed vac dried, dissolved in 160 μl Easyhyb buffer (Roche, 1 796 895), denatured (2 min, 96° C.), cooled to 50° C., applied on a pair of prehybridised slides (a+b, 80 μl/slide) prewarmed at 50° C., covered with a cover slide (Hybri slibs, Mol. Probes. H-18201) and incubated overnight at 42° C. in a humidified hybridization chamber (Corning 2551). Slides were washed (pair a+b in one 50 ml tube, 1× in 1×SSC/0.1% SDS 37° C., 1× in 0.5×SSC 37° C., 2× in 0.2×SSC 20° C.) and dried with N₂-gas. All pre-hybridisation buffers were 0.45 μm filtered to reduce dust noise. Slide images of Cy5- and Cy3-fluorescence intensity (ScanArray Express Scanner & Software, Packard Biosc.) were analysed (Imagene 5.6 Software, Biodiscovery) to obtain for each spot signal- and local background value (medians) for the hybridized Cy5-RNA and Cy3-reference gDNA. These values were used for further data analysis.

Array Data Normalization

Before normalization, all low abundant spots having a Signal/Background below 1.5 were removed. Data were normalized using a total cDNA signal correction. For each slide and each spot, the difference between signal and background was calculated for Cy5 and Cy3. Per slide, the sum of the differences was taken for Cy5 and Cy3, and the ratio between these two was used as normalisation factor for that particular slide. All spots (chromosomal and genomic) were normalised using this total cDNA signal.

Data Analysis of the Transcriptomics Data by Multivariate Regression Analysis Scaling

Data were range scaled [(x− x)/(x_(max)−x_(min))] (van den Berg et al., 2006, BMC Genomics 7:142) in the statistical analysis. Mathematically, range-scaling means that every element of column i is divided by the range of column i. The range of column i is the difference between the maximum and minimum value of all elements of column i. Subsequently, the scaled dataset is mean-centered. Mathematically, mean-centering means that adding up the values of the individual elements of column i of a data matrix results in zero for column i. This is achieved by subtracting the mean of column from all values of the individual elements of column i.

PLS Analysis

PLS analysis (Geladi and Kowalski, 1986) was performed in the Matlab environment using the PLS Toolbox (version 3.5.4, 2006; Eigenvector Research, Manson, Wash.).

It is possible that transcripts that show a lot of variation disturb the performance of the PLS model. Therefore, the model was optimized using a jack-knife approach. A model was build leaving out 10% of the samples, which was repeated until all samples were left out once. For each transcript, the relative standard deviation (RSD) was calculated and transcripts which had an RSD>50% were left out to build a second PLS model.

Validation of the Results

A double cross-validation procedure was used to validate the PLS model. In short, two loops are defined: an inner loop and an outer loop. In the innerloop 90% of the data is used to find an optimal PLS model. In the outerloop a prediction is made for the remaining 10% of the data based on the innerloop PLS model. This is repeated until all samples are left out once (so in this case 10 times). Goal of the DCV is to get an independent estimate of the prediction error. The R² was calculated to determine how good the original productivity or titer was predicted by the model. The closer the R² gets to 1, the better the model.

Sequence Analysis of Spots Selected after Transcriptomics Approach

The relevant clones were selected from the glycerol stocks of the ordered libraries (gDNA and cDNA library respectively) and cultivated in 96-well microtiter plates. The sequences of the inserts from both the 3′ and the 5′ end were determined by High Throuput (HT) sequencing service.

All RNA samples were labelled with Cy5. Hybridisations were performed with all 30 RNA samples, using Cy3-labeled chromosomal DNA of A. terreus as the reference.

The raw transcriptomics data were shown to be of high quality, based on visual inspection of the arrays after fluorescence scanning. Notably, also the hybridization with the partially degraded RNA samples gave good results.

The normalized data were subsequently combined. As the A. terreus array consisted out of two slides, different strategies of combining the data from the two slides were pursued, making use of the fact that the cDNA clones are present on both the A and B slide:

-   -   SET 1=mean expression signal of the cDNA clones on slide A and         B, take only those spots that give a signal on both the A and B         slide     -   SET 2=use only the signal of the cDNA spots on the A slide.         Spots with a Signal/Background below 1.5 were removed.     -   SET 3=use only the signal of the cDNA spots on the B slide.         Spots with a Signal/Background below 1.5 were removed.     -   SET 4=Combimean cDNA data of both the A and B slide;         -   i. If both measurement values were zero the combined value             was zero;         -   ii. If both measurements values were both non-zero, the             combined value was equal to the average of the two             measurement values;         -   iii. If one of the two measurement values was zero and the             other measurement value was non-zero, the combined value was             equal to the non-zero measurement value.     -   SET 5=SET 1+normalized gDNA spots using the normalization factor         calculated based on the cDNA clones.

The most relevant spots were subsequently identified by multivariate regression analysis, Multivariate data analysis (MVDA) tools seem very well suited to prioritize leads from functional genomics datasets. These tools take into account the inherent interdependency of biomolecules. These tools allow the identification of the specific genes that are the most important for a specific phenotype by determining the strength of the correlation of the expression of every gene with the biological question under study. Especially the regression tool partial least squares (PLS) holds great promise. Principally, the application of PLS results in a model (equation) that predicts a quantifiable phenotype of interest (e.g. itaconic acid titer, P) in terms of the transcripts (A, B, C, . . . ) expressed in A. terreus;

P=b ₁ A+b ₂ B+b ₃ C+ . . . .

By subsequently ordering the transcripts based on the absolute value of the regression values (i.e. b₁, b₂, b₃, . . . ) transcripts are identified that contribute the most to itaconate production.

PLS models with both the itaconate titers of the different samples and the itaconate productivity of the different samples were built using these different combined data sets. Moreover, not only linear models but also logarithmic models were built using the log of the itaconate titer (Table 4). Of these, only the (linear) itaconate titer models were reasonably good models as judged by the (double) cross validation results and the stability of these models (i.e. R² double cross validation≈0.4-0.5)(Table 4). The results of the other PLS models were very poor, and these models were not pursued.

TABLE 4 Overview of the PLS models build using the transcriptomics data set X Y R² double cross (data set) (Phenotype) validation PLS model SET 1 Productivity 0.10 Titer 0.51 Log(titer) 0.05 SET 2 Productivity 0.13 Titer 0.41 Log(titer) 0.18 SET 3 Productivity 0.08 Titer 0.45 Log(titer) 0.06 SET 4 Productivity 0.07 Titer 0.40 Log(titer) 0.12 SET 5 Productivity 0.08 Titer 0.38 Log(titer) 0.05

Moreover, a second PLS model was built with the titer as the Y-variable, using only the transcripts whose regression value had an RSD<50% (as determined based on jack-knifing) in the first PLS model. This were, in general, only some 10-20% of the spots of the complete data set.

‘Top 20’-ies of the combined data data sets analyzed by PLS using the itaconic acid titer as the phenotype were generated. These ‘top-20’-ies were combined, and unique spots were identified (Table 5 and 6). In total 102 of the most relevant spots obtained after PLS analyses (based on 10 models; 5 data sets, 2 PLS models per data set) were selected for sequencing.

Of the selected spots, >92% were spots belonging to cDNA clones. However, also four of the 5 combined data sets contained only cDNA clones (see above).

Following sequence analysis of the 102 selected spots, the genes present on these inserts were identified by performing a homology search using BLAST based on the draft version of the A. terreus genome sequence as available from the BROAD institute (http://www.broad.mit.edu/annotation/fgi/).

As different combined data sets/'top 20′-ies were generated, the overall ranking of the transcripts, as reported in Table 5 was based on:

-   -   (i) The frequency of occurrence of an individual spot in the top         20 of the different combined data sets analyzed     -   (ii) The sum of the overall rank of a spot in the different ‘top         20’-ies of the different combined data sets.

Table 5 shows the results of the genes identified on the 20 highest overall ranking spots identified by PLS analysis based on titer.

TABLE 5 Overall Top 20 PLS analysis - itaconic acid titer. Rank Clone ID Gene locus Gene name 1 AsTeR010H08 2 AsTeR037H12 3 AsTeR053F06 4 AsTeR037C07 5 AsTeR007H08 6 AsTeR048G12 7 AsTeR023B07 8 AsTeR033F08 9 AsTeR035E10 10 AsTeR033A04 11 AsTeR029F07 12 AsTeR045A05 13 AsTeR010H12 14 AsTeR041C10 15 AsTeR030D01 ATEG_09972.1 Predicted protein 16 AsTeR009D10 17 AsTeR032E02 18 AsTeR032H04 19 AsTeR004H04 20 AsTeR054B06

Moreover, a ranked list of the genes that were identified with the highest frequency amongst the in total 190 clones sequenced (i.e. 102 spots selected after PLS analyses and 88 spots obtained after the differential analyses—See EP 08151584)(Table 6).

TABLE 6 Most frequently identified genes amongst the 190 clones sequenced # clones # clones Regulation under from from itaconate differential PLS producing Freq. Gene locus approach approach conditions Gene name 25 ATEG_09970.1 25 Up mitochondrial tricarboxylic acid transporter - EP08151584 19 15 ATEG_09971.1 14 1 Up cis-aconitate decarboxylase (EP 07112895) 14 11 7 7 4 3 3 2 ATEG_09972.1 2 Up Predicted protein 2 2 2 2 2 2 2 2 The ATEG_00972.1 gene, flanking cis-aconitate decarboxylase (ATEG_09971.1 - EP 07112895), and the putative mitochondrial tricarboxylate transporter protein (ATEG_09970.1 - EP08151584) were identified on two of the spots identified by PLS analysis (Table 6) and had an overall rank of 15 in the combined top 20 (Table 5). Just as the CAD gene and the MTAT gene, the ATEG_09972.1 gene, was found to be upregulated under itaconic acid producing environmental conditions.

Example 4 Homology Analysis of the ATEG_(—)09972.1 Gene

A BLAST search was performed in order to identify homologous to the predicted protein ATEG_(—)09972.1 (Table 7). High homologies were only found with genes from two other A. terreus strains. With other micro-organisms and more specifically fungi, homologues were found although with a relatively low homology. Based on the annotation of these homologous genes and the major facilitator superfamily domain identified in this gene, ATEG_(—)09972.1 was identified as an itaconate exporter.

TABLE 7 BLAST search results with ATEG_09972.1 Identity/ Rank Protein Best Hit E value Similarity 1 Predicted protein XP_001209274.1 0.0 100%/100% A. terreus 2 unknown AAD34564.1 0.0 92%/93% A. terreus 3 Unnamed protein BAE57135.1 2e−160 70%/84% product A. oryzae 4 putitative MFS XP_749665.1 5e−135 64%/77% transporter A. fumigatus 5 putitative MFS XP_001260160.1 5e−134 65%/79% transporter N. fischeri 6 Hypothetical protein XP_680781.1 5e−123 59%/74% AN7512.2 A. nidulans 7 Hypothetical protein XP_663623.1 1e−105 52%/68% AN6019.2 A. nidulans 8 Unnamed protein BAE61268.1 1e−91  45%/61% product A. oryzae 9 pH-responsive XP_001215904.1 2e−91  68%/81% protein 2 precursor A. terreus 10 hypothetical XP_383000.1 1e−81  47%/63% protein Fgo2824.1 G. zeae

It appears that at least the gene coding for the cis-aconitate decarboxylase (ATEG_(—)09971.1) and the gene encoding the mitochondrial tricarboxylate transporter (ATEG_(—)9970.1) lie in the same cluster in the A. terreus genome (FIG. 2).

A gene neighbouring CAD, the mitochondrial tricarboxylate transporter and the itaconate exporter is a putative regulator containing a zinc-finger domain (ATEG_(—)09969.1). This gene was not identified using our transcriptomics approach, but considering its localization it is expected that it is relevant for itaconic acid synthesis FIG. 2 shows that also the lovastatin pathway genes are located on this cluster, suggesting a link between both pathways which are (mainly) specific for A. terreus.

Example 5 (Co-)Expression of the ATEG_(—)09972.1 Gene in Aspergillus Niger

In order to unambiguously establish that the ATEG_(—)09972.1 protein aids to the increased production of itaconic acid, a naturally non-itaconic acid producing fungal host was (co-)transformed with the CAD gene or transformed with the CAD and MTT (ATEG_(—)09970.1) gene were co-transformed with the ATEG_(—)09972.1 (MFS) gene.

Expression of the CAD (ATEG 09971.1) Gene in Aspergillus Niger

A PCR generated copy of the gene encoding the CAD protein (see EP07112895) was generated. For this purpose two sets of primers were generated as shown below. PCR amplification based on A. terreus NRRL1960 genomic DNA resulted in the isolation of PCR fragments from which the complete coding region of the gene encoding the CAD protein, could be isolated as BspHI-BamHI fragments.

CAD full sequence 1529 bp ORIGIN          BspHI  cadfor40° C.     5′-ATCGTCATGACCAAGCAATCTG-3′          BspHI  cadfor53° C.     5′-ATCGTCATGACCAAGCAATCTGCGGACA-3′ 1 ATGACCAAGC AATCTGCGGA CAGCAACGCA AAGTCAGGAG TTACGTCCGA AATATGTCAT 61 TGGGCATCCA ACCTGGCCAC TGACGACATC CCTTCGGACG TATTAGAAAG AGCAAAATAC 121 CTTATTCTCG ACGGTATTGC ATGTGCCTGG GTTGGTGCAA GAGTGCCTTG GTCAGAGAAG 181 TATGTTCAGG CAACGATGAG CTTTGAGCCG CCGGGGGCCT GCAGGGTGAT TGGATATGGA 241 CAGgtaaatt ttattcactc tagacggtcc acaaagtata ctgacgatcc ttcgtatagA                           (intron) 301 AACTGGGGCC TGTTGCAGCA GCCATGACCA ATTCCGCTTT CATACAGGCT ACGGAGCTTG 361 ACGACTACCA CAGCGAAGCC CCCCTACACT CTGCAAGCAT TGTCCTTCCT GCGGTCTTTG 421 CAGCAAGTGA GGTCTTAGCC GAGCAGGGCA AAACAATTTC CGGTATAGAT GTTATTCTAG 481 CCGCCATTGT GGGGTTTGAA TCTGGCCCAC GGATCGGCAA AGCAATCTAC GGATCGGACC 541 TCTTGAACAA CGGCTGGCAT TGTGGAGCTG TGTATGGCGC TCCAGCCGGT GCGCTGGCCA 601 CAGGAAAGCT CTTCGGTCTA ACTCCAGACT CCATGGAAGA TGCTCTCGGA ATTGCGTGCA 661 CGCAAGCCTG TGGTTTAATG TCGGCGCAAT ACGGAGGCAT GGTAAAGCGT GTGCAACACG 721 GATTCGCAGC GCGTAATGGT CTTCTTGGGG GACTGTTGGC CCATGGTGGG TACGAGGCAA 781 TGAAAGGTGT CCTGGAGAGA TCTTACGGCG GTTTCCTCAA GATGTTCACC AAGGGCAACG 841 GCAGAGAGCC TCCCTACAAA GAGGAGGAAG TGGTGGCTGG TCTCGGTTCA TTCTGGCATA 901 CCTTTACTAT TCGCATCAAG CTCTATGCCT GCTGCGGACT TGTCCATGGT CCAGTCGAGG 961 CTATCGAAAA CCTTCAGGGG AGATACCCCG AGCTCTTGAA TAGAGCCAAC CTCAGCAACA 1021 TTCGCCATGT TCATGTACAG CTTTCAACGG CTTCGAACAG TCACTGTGGA TGGATACCAG 1081 AGGAGAGACC CATCAGTTCA ATCGCAGGGC AGATGAGTGT CGCATACATT CTCGCCGTCC 1141 AGCTGGTCGA CCAGCAATGT CTTTTGTCCC AGTTTTCTGA GTTTGATGAC AACCTGGAGA 1201 GGCCAGAAGT TTGGGATCTG GCCAGGAAGG TTACTTCATC TCAAAGCGAA GAGTTTGATC 1261 AAGACGGCAA CTGTCTCAGT GCGGGTCGCG TGAGGATTGA GTTCAACGAT GGTTCTTCTA 1321 TTACGGAAAG TGTCGAGAAG CCTCTTGGTG TCAAAGAGCC CATGCCAAAC GAACGGATTC 1381 TCCACAAATA CCGAACCCTT GCTGGTAGCG TGACGGACGA ATCCCGGGTG AAAGAGATTG 1441 AGGATCTTGT CCTCGGCCTG GACAGGCTCA CCGACATTAG CCCATTGCTG GAGCTGCTGA 1501 ATTGCCCCGT AAAATCGCCA CTGGTATAA                     cadrev42° C.     BamHI               3′-TTTAGCGGTGACCATATTCCTAGGCCCT-5′                    cadrev52° C.      BamHI          3′-GGCA

TTTAGCGGTGACCATATTCCTAGGCCCC-5′

Translation of Cad Encoding Gene

Total amino acid number: 490, MW=52710

1 M T K Q S A D S N A K S V T S E E I C H 21 W A S N L A T D D I P S D V L E R A K Y 41 L I L D G I A C A W V G A R V P W S E K 61 Y V Q A T M S F E P P G A C R V I G Y G 81 Q K L G P V A A A M T N S A F I Q A T E 101 L D D Y H S E A P L H S A S I V L P A V 121 F A A S E V L A E Q G K T I S G I D V I 141 L A A I V G F E S G P R I G K A I Y G S 161 D L L N N G W H C G A V Y G A P A G A L 181 A T G K L F G L T P D S M E D A L G I A 201 C T Q A C G L M S A Q Y G G M V K R V Q 221 H G F A A R N G L L G G L L A H G G Y E 241 A M K G V L E R S Y G G F L K M F T K G 261 N G R E P P Y K E E E V V A G L G S F W 281 H T F T I R I K L Y A C C G L V H G P V 301 E A I E N L Q G R Y P E L L N R A N L S 321 N I R H V H V Q L S T A S N S H C G W I 341 P E E R P I S S I A G Q M S V A Y I L A 361 V Q L V D Q Q C L L S Q F S E F D D N L 381 E R P E V W D L A R K V T S S Q S E E F 401 D Q D G N C L S A G R V R I E F N D G S 421 S I T E S V E K P L G V K E P M P N E R 441 I L H K Y R T L A G S V T D E S R V K E 461 I E D L V L G L D R L T D I S P L L E L 481 L N C P V K S P L V *

The resulting BspHI-BamHI fragment was cloned into the Aspergillus expression vector pAN52-4-amdS derived from Aspergillus expression vector pAN52-4. The Aspergillus expression vector pAN52-4-amdS was derived by cloning the Aspergillus selection marker amdS into the Aspergillus expression vector pAN52-4 (EMBL accession #Z32699).

Subsequently, an Aspergillus niger strain AB1.13 (Mattern, I. E. et al., 1992, Mol. Gen. Genet. 234:332-336) was transformed with the CAD expression vector. AmdS transformants resulting for this experiment were purified by single colony purification and retested for their AmdS+ phenotype.

Co-Expression of the CAD Gene and the ATEG 09970.1 Gene in Aspergillus Niger

The ATEG_(—)09970.1 gene (MTT) was synthesized (GeneArt) and cloned into Aspergillus niger expression vector pAN52-5doubleNotI by restriction enzyme cutting sites of double NotI. The expression vector pAN52-5doubleNotI was derived by adding an extra NotI site in the Aspergillus expression vector pAN52-4 (EMBL accession #Z32699). Moreover, the codons of the clone were optimized for expression in the Aspergillus niger strain.

Translation of MTT Cds

Universal code Total amino acid number: 286, MW=31503 Max ORF starts at AA pos 1 (may be DNA pos 1) for 286 AA (858 bases), MW=31503

1 ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCT 1  M  S  I  Q  H  F  R  V  A  L  I  P  F  F  A  A  F  C  L  P 61 GTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCA 21  V  F  A  H  P  E  T  L  V  K  V  K  D  A  E  D  Q  L  G  A 121 CGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCC 41  R  V  G  Y  I  E  L  D  L  N  S  G  K  I  L  E  S  F  R  P 181 GAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCC 61  E  E  R  F  P  M  M  S  T  F  K  V  L  L  C  G  A  V  L  S 241 CGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTG 81  R  I  D  A  G  Q  E  Q  L  G  R  R  I  H  Y  S  Q  N  D  L 301 GTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTA 101  V  E  Y  S  P  V  T  E  K  H  L  T  D  G  M  T  V  R  E  L 361 TGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATC 121  C  S  A  A  I  T  M  S  D  N  T  A  A  N  L  L  L  T  T  I 421 GGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTT 141  G  G  P  K  E  L  T  A  F  L  H  N  M  G  D  H  V  T  R  L 481 GATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATG 161  D  R  W  E  P  E  L  N  E  A  I  P  N  D  E  R  D  T  T  M 541 CCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCT 181  P  V  A  M  A  T  T  L  R  K  L  L  T  G  E  L  L  T  L  A 601 TCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGC 201  S  R  Q  Q  L  I  D  W  M  E  A  D  K  V  A  G  P  L  L  R 661 TCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCT 221  S  A  L  P  A  G  W  F  I  A  D  K  S  G  A  G  E  R  G  S 721 CGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTAC 241  R  G  I  I  A  A  L  G  P  D  G  K  P  S  R  I  V  V  I  Y 781 ACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCC 261  T  T  G  S  Q  A  T  M  D  E  R  N  R  Q  I  A  E  I  G  A 841 TCACTGATTAAGCATTGGTAA 281  S  L  I  K  H  W  *

Subsequently, an Aspergillus niger strain AB1.13 (Mattern, I. E. et al., 1992, Mol. Gen. Genet. 234:332-336) was co-transformed with the CAD expression vector and the MTT expression vector. AmdS transformants resulting for this experiment were purified by single colony purification and retested for their AmdS+ phenotype.

Co-Expression of the Cad Gene, MTT Gene (ATEG 09970.1) Together with the ATEG-09972.1 Gene in Aspergillus Niger

The ATEG-09972.1 (MFS) gene was synthesized (GeneArt) and cloned into Aspergillus niger expression vector pAN52-5doubleNotI by restriction enzyme cutting sites of double NotI. The expression vector pAN52-5doubleNotI was derived by adding an extra NotI site in the Aspergillus expression vector pAN52-4 (EMBL accession #Z32699). Moreover, codons of the clone were optimized for expression in the Aspergillus niger strain.

Translation of MFS cds (1-861)

Universal code Total amino acid number: 286, MW=31503 Max ORF starts at AA pos 1 (may be DNA pos 1) for 286 AA (858 bases), MW=31503

1 ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCT 1  M  S  I  Q  H  F  R  V  A  L  I  P  F  F  A  A  F  C  L  P 61 GTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCA 21  V  F  A  H  P  E  T  L  V  K  V  K  D  A  E  D  Q  L  G  A 121 CGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCC 41  R  V  G  Y  I  E  L  D  L  N  S  G  K  I  L  E  S  F  R  P 181 GAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCC 61  E  E  R  F  P  M  M  S  T  F  K  V  L  L  C  G  A  V  L  S 241 CGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTG 81  R  I  D  A  G  Q  E  Q  L  G  R  R  I  H  Y  S  Q  N  D  L 301 GTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTA 101  V  E  Y  S  P  V  T  E  K  H  L  T  D  G  M  T  V  R  E  L 361 TGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATC 121  C  S  A  A  I  T  M  S  D  N  T  A  A  N  L  L  L  T  T  I 421 GGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTT 141  G  G  P  K  E  L  T  A  F  L  H  N  M  G  D  H  V  T  R  L 481 GATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATG 161  D  R  W  E  P  E  L  N  E  A  I  P  N  D  E  R  D  T  T  M 541 CCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCT 181  P  V  A  M  A  T  T  L  R  K  L  L  T  G  E  L  L  T  L  A 601 TCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGC 201  S  R  Q  Q  L  I  D  W  M  E  A  D  K  V  A  G  P  L  L  R 661 TCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCT 221  S  A  L  P  A  G  W  F  I  A  D  K  S  G  A  G  E  R  G  S 721 CGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTAC 241  R  G  I  I  A  A  L  G  P  D  G  K  P  S  R  I  V  V  I  Y 781 ACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCC 261  T  T  G  S  Q  A  T  M  D  E  R  N  R  Q  I  A  E  I  G  A 841 TCACTGATTAAGCATTGGTAA 281  S  L  I  K  H  W  *

Subsequently, an Aspergillus niger strain AB1.13 (Mattern, I. E. et al., 1992, Mol. Gen. Genet. 234:332-336) was co-transformed with the CAD expression vector, the MTT expression vector and the MFS expression vector. AmdS transformants resulting for this experiment were purified by single colony purification and retested for their AmdS+ phenotype.

Analysis of A. Niger Transformants for Itaconic Acid Production

Several positive transformants and the parental host strain were subsequently cultured in Shake Flask in MM medium supplied with uridine containing glucose as C-source and nitrate as N-source. Medium samples from the various cultures were analyzed by HPLC for the presence of itaconic acid (Table 8).

Shake flask medium compositions: Per litre: 0.52 g of KCl, 2.4 g of NaNO₃, 1.56 g of KH₂PO₄, 0.24 g of MgSO₄*7H₂O, 5 mg of Fe(III) SO₄*7H₂O, 5 mg of MnCl₂*4H₂O, 0.022 g of ZnSO₄*7H₂O, 0.011 g of H₃BO₃, 1.7 mg of CoCl₂*6H₂O and 2.44 g of uridine, 100 g of glucose as a carbon source. All media were prepared in demineralised water.

HPLC analysis was performed with a reversed phase column, using a Develosil™ 3 μm R^(P)-Aqueous C30 140A column at a constant temperature of 25° C., with elution with 20 mM NaH2PO4, pH 2.25 and acetonitril. Compounds were detected by UV at 210 nm using a Waters 2487 Dual wavelength Absorbance detector (Milford, Mass., USA). Retention time of itaconic acid was 18.82 min.

TABLE 8 Itaconic acid concentration in the culture fluid of the A. niger AB1.13 transformants cultivated in shake flasks. Aspergillus niger AB 1.13 transformants (AB 1.13 CAD) itaconic acid strain code time (hrs) mg/g wet weight AB 1.13 WT 54 0 AB 1.13 CAD 5.1 54 1.0 AB 1.13 CAD 7.2 54 0.7 AB 1.13 CAD 10.1 54 1.4 AB 1.13 CAD 14.2 54 1.2 AB 1.13 CAD 16.1 54 1.2 AB 1.13 CAD + MTT 4.1 54 1.3 AB 1.13 CAD + MTT 6.2 54 1.5 AB 1.13 CAD + MTT 2.2.1  54 2.2 AB 1.13 CAD + MTT + MFS 9.2.1* 54 2.3 AB 1.13 CAD + MTT + MFS 9.2.2* 54 2.5 AB 1.13 CAD + MTT + MFS 9.4.1* 54 2.5 AB 1.13 CAD + MTT + MFS 12.1.1  54 2.3 *Duplicate isolates of the same transformant.

No itaconic acid was detected in the supernatant of the parental strain while in the culture fluid of the strains containing the CAD gene (strains marked CAD), itaconic acid was detected.

In both the culture fluid of the strains containing the CAD gene and the strains containing both the CAD gene and MTT gene (strains marked CAD+MTT) and the strains containing the CAD, the MTT and the MFS gene (strains marked CAD+MTT+MFS), itaconic acid was detected (Table 8). In all MFS expressing strains more itaconic acid was produced in the culture fluid than in the strains expressing only the CAD gene, or the CAD and the MTT gene. Moreover, the average itaconic acid concentration was higher in the culture fluid of the strains expressing the MFS, the CAD and the MTT gene compared to the transformants expressing only the CAD or the CAD+MTT gene: 2.4 mg itaconic acid/g mycelial wet weight versus 1.1 mg itaconic acid/g mycelial wet weight (CAD gene only) and 1.7 mg itaconic acid/g mycelial wet weight (CAD+MTT gene—Table 8). 

1. A nucleic acid molecule encoding a protein encoded by an itaconate transporting Major Facilitator Superfamily Transporter (MFST) gene sequence.
 2. A nucleic acid molecule according to claim 1, wherein the nucleic acid molecule comprises the sequence of ATEG_(—)09972.1 as depicted in FIG. 3 b, or a sequence more than 70% identical thereto.
 3. A protein encoded by the nucleic acid molecule according to claim
 1. 4. A method for the production of itaconic acid in a micro-organism comprising increasing the activity of an itaconate transporter protein.
 5. A method according to claim 4, wherein the increasing is effected by the expressing of a nucleic acid molecule according to claim
 1. 6. A method according to claim 1, wherein the gene sequence is derived from A. terreus, A. niger, A. nidulans, A. oryzae, or A. fumigates.
 7. A method according to claim 4, wherein the micro-organism is a citrate producing micro-organism.
 8. A method according to claim 4, wherein the micro-organism is a lovastatin producing micro-organism.
 9. A method according to claim 4, wherein the expressing is effected by providing a vector comprising a promoter operably linked to a nucleic acid sequence encoding said transporter protein.
 10. A method according to claim 4, wherein said micro-organism is also provided with a nucleic acid molecule encoding an enzyme that catalyses the formation of cis-aconitate.
 11. A method according to claim 4, wherein said micro-organism is also provided with a nucleic acid molecule encoding cis-aconic acid decarboxylase (CAD).
 12. A method according to claim 4, wherein said micro-organism is also provided with a nucleic acid sequence encoding a protein capable of transporting di/tricarboxylic acids from the mitochondrion.
 13. A method according to claim 4, wherein the expression of the zinc-finger regulator protein, encoded by the nucleic acid sequence present in ATEG_(—)09969.1 is modulated in said micro-organism.
 14. A method according to claim 4, further comprising isolating itaconic acid from the extracellular medium.
 15. Host cell wherein a nucleic acid is introduced that encodes a protein that transports dicarboxylic acids from the cytosol to the extracellular medium.
 16. Host cell according to claim 15, wherein said protein transports itaconic acid.
 17. Host cell according to claim 15, wherein said protein is encoded by a nucleic acid molecule comprising the sequence of ATEG_(—)09972.1 as depicted in FIG. 3 b, or a sequence more than 70% identical thereto.
 18. Host cell according to claim 15, wherein said host cell is A. niger or A. terreus.
 19. Host cell according to claim 15, wherein a nucleic acid molecule encoding the enzyme CAD is co-introduced.
 20. Host cell according to claim 15, wherein a nucleic acid sequence encoding a protein capable of transporting di/tricarboxylic acids from the mitochondrion is co-introduced). 21-24. (canceled)
 25. The method of claim 7 wherein the citrate producing microorganism is A. terreus, A. niger, A. itaconicus, A. nidulans, A. oryzae, A. fumigates, Yarrowia lipolytica, Ustilago zeae, Candida sp., Rhodotorula sp., Pseudozyma antarctica, E. coli, or Saccharomyces cerevisiae.
 26. The method of claim 8 wherein the lovastatin producing microorganism is Monascus spp., Penicillium spp., Hypomyces spp., Dotatomyces spp., Phoma spp., Eupenicillium spp., Gymnoascus spp., Pichia labacenis, Candida cariosilognicola, Paecilomyces virioti, Scopulariopsis brevicaulis or Trichoderma spp.
 27. The method of claim 11 wherein the nucleic acid molecule encoding CAD comprises the nucleic acid sequence comprised in ATEG_(—)09971.1.
 28. The method of claim 12 wherein the nucleic acid molecule encoding said protein comprises the nucleic acid comprised in ATEG_(—)09970.1.
 29. The host cell of claim 19 wherein the nucleic acid molecule encoding CAD comprises the nucleic acid sequence comprised in ATEG_(—)09971.1.
 30. The host cell of claim 20 wherein the nucleic acid molecule encoding said protein comprises the nucleic acid sequence comprised in ATEG_(—)09970.1. 